Changed code where variable used for getopt is then reused by later code for completely different purpose.
razf_read and razf_write are intended to replace system calls of read and write respectively and thus their method signature should match.
Tweak method definitions of knet_read and knet_write to better match system read and write.
Add const modifier to certain global constants.
Add static modifier to global constants where possible.
Delete unused constants
Be consistent about using float or double in errmod depcorr
Adjust position of fileret in _razf_read and ensure correct variable is returned.
Fix bgzf read and write prototypes to better match system ones, length is size_t not ssize_t
Add comments, make variable names more meaningful and clean up a few things in bcftools (including some spaces that crept in that should have been tabs).
Use off_t and lseek rather than the 64 alternatives as this is more portable.
Fix signed return going into unsigned variable
Cleanup and add comments to genotype calling code
Follow per-file convention for using either tabs or spaces
samtools mpileup/bcftools view: Fix of integer overflow at very high depths with many samples. Added MQ0 annotation.